MK5 Microarray Data

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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Gene	Filtered	Value Type	Rank	description	green	Interaction Map	network_comparison	red	Network Comparison Type

Results: HTML CSV LaTeX

Showing element 1 to 50 of 77072 in total

Filtered  : 0
Value Type  : Measured

Rank	description	green	Interaction Map	network_comparison	red	Network Comparison Type
1	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	High confidence	6325	85	Subtracted
			Low confidence
	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]	0.00001	High confidence	36400000	364	Divided
			Low confidence
2	cab2. [refseq;acc:nm_033419]	174	High confidence	17400000	0.00001
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	89	Low confidence	8900000
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	High confidence	6325	85	Subtracted
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	Low confidence	4196.8	23818.1
3	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89		8900000	0.00001	Divided
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	19621.3	High confidence	4196.8	23818.1	Subtracted
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	Low confidence	2393.82	5106.93
	pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129]	109	High confidence	10900000	0.00001	Divided
4	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801]	4356	Low confidence	2274	2082	Subtracted
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89		8900000	0.00001	Divided
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		High confidence
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	21730		3026	18704	Subtracted
5	histone h4. [swissprot;acc:p02304]	24446.3		2673.2	21773.1
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	89		8900000	0.00001	Divided
	jumonji protein. [swissprot;acc:q92833]	17.5166	Low confidence	1751660
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	2740.13		2254.84	485.286	Subtracted
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	89	High confidence	8900000	0.00001	Divided
	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	0.00001	Low confidence	1300000	13
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	8836.85		1244.48	7592.37	Subtracted
		15605.1	High confidence	2430.4	13174.7
7	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	5898.71	Low confidence	1238.62	4660.09
	sedlin. [swissprot;acc:o14582]	43	High confidence	4300000	0.00001	Divided
	tbc1 domain family, member 8 (with gram domain); vascular rab-gap/tbc-containing. [refseq;acc:nm_007063]	0.00001	Low confidence	231962	2.31962
	zinc finger protein 277. [swissprot;acc:q9nrm2]	15605.1	High confidence	2430.4	13174.7	Subtracted
8	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410	Low confidence	75.4118	85	Divided
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	7500.75	High confidence	2393.82	5106.93	Subtracted
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	43		4300000	0.00001	Divided
	zinc finger protein 277. [swissprot;acc:q9nrm2]	8770.72	Low confidence	1232.83	7537.89	Subtracted
9	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	11468.3		1212.6	10255.7
		14756	High confidence	2278	12478
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	6410		75.4118	85	Divided
	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]	10.6048	Low confidence	36.1876	383.762
10	dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2804		1211	1593	Subtracted
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	6410	High confidence	75.4118	85	Divided
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	6193.07		1637.55	7830.62	Subtracted
	serpin b12. [swissprot;acc:q96p63]	5.56738	Low confidence	35.8425	199.549	Divided
11	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	7252.02	High confidence	1517.74	5734.28	Subtracted
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	5341.81	Low confidence	1111.45	4230.36
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669		34.8539	199.249	Divided
	serpin b12. [swissprot;acc:q96p63]	5.56738	High confidence	35.8425	199.549
12	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	7099.51		1469.89	5629.62	Subtracted
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	5.71669		34.8539	199.249	Divided
	mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849]	58	Low confidence	14.8103	859
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	30022.4		1099.6	31122	Subtracted
13	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]	47	High confidence	29	1363	Divided
				1316		Subtracted

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.